Contacts of the helix formed by residues 71 - 87 (chain A) in PDB entry 3NSI
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 71 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A PHE* 4.1 3.6 - - - -
27A TYR 3.9 9.2 - - - +
28A LYS* 4.2 19.5 - - - -
69A GLU 3.0 6.8 + - - +
70A VAL* 1.3 75.5 - - - +
72A PHE* 1.3 66.6 + - - +
73A VAL* 3.4 13.5 + - - +
74A GLU* 2.8 28.2 + - - +
75A TYR* 2.9 21.1 + - - +
95B SER* 4.4 15.3 + - - +
98B PRO* 5.0 4.9 - - - +
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Residues in contact with PHE 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 4.3 4.7 - - + -
13A VAL* 3.6 37.0 - - + -
16A PHE* 3.7 22.9 - + + -
27A TYR 4.3 1.6 + - - -
71A ASP* 1.3 73.8 - - - +
73A VAL* 1.3 59.0 + - - +
75A TYR* 3.1 33.0 + + - +
76A VAL* 2.9 50.1 + - + +
80B ALA* 3.7 19.1 - - + -
83B CYS* 3.4 26.2 - - + -
84B LEU* 4.4 13.0 - - + -
90B PHE* 3.3 37.5 - + + -
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Residues in contact with VAL 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ASP* 3.3 10.8 + - - +
72A PHE* 1.3 76.5 - - - +
74A GLU* 1.3 58.4 + - - +
76A VAL* 3.3 3.6 + - - +
77A ARG* 2.9 29.1 + - + +
77B ARG* 4.8 19.2 - - + -
80B ALA* 4.3 21.4 - - + +
81B CYS* 5.3 0.7 - - - -
84B LEU* 3.8 21.1 - - + -
98B PRO* 3.2 38.6 - - + -
99B CYS* 4.8 3.8 - - - -
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Residues in contact with GLU 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLN* 3.8 21.0 + - - +
34A LEU* 5.1 3.6 - - + +
69A GLU* 3.9 7.4 - - - +
70A VAL* 3.8 25.8 + - + +
71A ASP* 2.8 25.6 + - - +
73A VAL* 1.3 72.2 - - - +
75A TYR* 1.3 65.5 + - - +
77A ARG* 3.2 37.9 + - - +
78A SER* 3.0 22.5 + - - -
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Residues in contact with TYR 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 2.8 52.3 + - + +
15A THR* 3.7 14.2 - - - +
16A PHE* 3.5 35.9 - + + -
29A LEU* 4.6 1.1 - - + -
34A LEU* 4.0 18.4 - - + -
37A LEU* 3.5 32.3 - - + -
70A VAL* 4.0 12.2 - - + +
71A ASP 2.9 12.2 + - - +
72A PHE* 3.2 17.5 - + - +
74A GLU* 1.3 77.1 - - - +
76A VAL* 1.3 69.2 + - + +
78A SER* 2.5 27.5 + - - -
79A LEU* 3.3 17.9 + - + +
5B LEU* 3.8 8.7 - - - +
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Residues in contact with VAL 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 4.2 11.0 - - + -
72A PHE* 2.9 52.3 + - + +
73A VAL 3.8 4.0 - - - +
75A TYR* 1.3 85.1 - - + +
77A ARG* 1.3 66.5 + - - +
79A LEU* 3.1 13.5 + - + +
80A ALA* 3.0 20.1 + - - +
12B ILE* 6.2 0.2 - - + -
76B VAL* 2.9 40.4 - - + +
77B ARG* 5.1 0.4 - - - +
79B LEU* 5.7 1.3 - - + -
80B ALA* 4.0 11.2 - - + +
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Residues in contact with ARG 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A PHE* 5.8 4.2 - - - -
73A VAL* 2.9 16.5 + - + +
74A GLU* 3.2 49.5 + - - +
76A VAL* 1.3 77.8 - - - +
78A SER* 1.3 57.4 + - - +
80A ALA* 3.2 7.7 + - - +
81A CYS* 2.9 29.4 + - - -
98A PRO* 5.6 1.3 - - - -
99A CYS* 3.2 37.5 + - - +
73B VAL* 4.6 19.3 - - + -
76B VAL* 5.3 0.9 - - - -
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Residues in contact with SER 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 3.7 28.7 - - - +
38A LEU* 4.0 10.8 - - - +
58A PHE* 3.8 27.1 - - - -
74A GLU 3.0 12.7 + - - -
75A TYR 2.5 20.9 + - - -
77A ARG* 1.3 77.1 - - - +
79A LEU* 1.3 56.7 + - - +
81A CYS* 3.2 4.1 + - - +
82A LEU* 2.9 35.1 + - - +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ILE* 3.8 43.3 - - + -
38A LEU* 3.6 27.8 - - + -
42A LEU* 4.0 14.5 - - + +
75A TYR* 3.5 29.4 - - + +
76A VAL* 3.1 13.1 + - + +
78A SER* 1.3 82.3 + - - +
80A ALA* 1.3 62.9 + - - +
82A LEU* 3.1 8.7 + - - +
83A CYS* 3.1 26.8 + - - -
5B LEU* 4.1 13.7 - - + -
9B VAL* 4.3 16.2 - - + +
76B VAL* 5.7 0.9 - - + -
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Residues in contact with ALA 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76A VAL 3.0 12.3 + - - +
77A ARG* 3.4 11.0 - - - +
79A LEU* 1.3 77.2 - - - +
81A CYS* 1.3 62.1 + - - +
83A CYS* 3.0 14.9 + - - +
84A LEU* 3.1 14.7 + - - +
72B PHE* 3.8 20.4 - - + -
73B VAL* 4.3 17.7 - - + +
76B VAL* 4.0 28.1 - - + +
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Residues in contact with CYS 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58A PHE* 4.4 11.9 - - + -
77A ARG* 2.9 22.1 + - - -
78A SER* 3.5 10.8 - - - +
80A ALA* 1.3 76.4 - - - +
82A LEU* 1.3 62.1 + - - +
84A LEU* 3.2 5.4 + - - +
85A TYR* 3.0 39.7 + - + -
98A PRO* 5.2 0.2 - - - -
99A CYS* 2.0 68.0 - - - -
73B VAL* 5.2 0.9 - - - -
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Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 3.7 24.9 - - + +
42A LEU* 3.4 35.7 - - + -
45A TRP* 4.2 10.9 - - + -
55A TYR* 4.7 15.3 - - + +
58A PHE* 3.2 39.3 - - + -
59A MET* 4.9 5.6 - - - -
78A SER 2.9 13.1 + - - +
79A LEU* 3.1 9.8 + - - +
81A CYS* 1.3 76.1 - - - +
83A CYS* 1.3 56.8 + - - +
85A TYR* 4.1 7.4 - - + -
86A CYS* 2.8 37.2 + - - +
9B VAL* 6.4 0.2 - - + -
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Residues in contact with CYS 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TRP* 3.9 11.2 - - - -
79A LEU 3.1 13.5 + - - -
80A ALA* 3.0 9.9 + - - +
82A LEU* 1.3 75.0 - - - +
84A LEU* 1.3 62.8 + - - +
87A HIS* 2.8 34.4 + - + +
90A PHE* 3.8 5.8 - - + -
9B VAL* 3.1 36.6 - - - -
13B VAL* 3.6 22.9 - - + -
72B PHE* 3.5 22.9 - - + -
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A THR* 4.6 1.4 + - - -
51A ARG* 2.6 34.8 + - - +
80A ALA 3.1 11.5 + - - +
81A CYS 3.2 6.7 + - - +
83A CYS* 1.3 78.3 - - - +
85A TYR* 1.3 65.0 + - + +
87A HIS 4.7 1.2 - - - +
90A PHE* 3.5 43.8 - - + +
93A CYS* 4.8 10.5 - - - -
95A SER* 4.7 8.7 - - - +
97A PRO* 4.2 8.1 - - + -
98A PRO* 3.6 31.0 - - + -
99A CYS* 4.2 6.7 - - - -
72B PHE* 4.3 12.3 - - + -
73B VAL* 3.9 13.7 - - + -
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Residues in contact with TYR 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A PRO* 3.2 2.4 - - - +
48A THR* 2.7 39.4 + - - -
51A ARG* 3.6 13.8 - - + +
54A ASP* 3.4 30.6 + - + +
55A TYR* 4.0 27.1 - + + -
58A PHE* 3.7 31.7 - + + +
81A CYS* 3.0 29.9 + - + +
82A LEU* 3.8 9.9 - - + +
84A LEU* 1.3 80.7 - - - +
86A CYS* 1.3 61.0 + - - +
87A HIS 3.8 0.2 - - - -
97A PRO* 2.9 47.2 - - + +
99A CYS* 3.9 9.0 - - - +
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Residues in contact with CYS 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TRP* 4.0 24.2 - - + -
46A THR 3.2 46.1 + - - +
47A PRO* 3.5 4.7 - - - -
48A THR* 4.0 7.5 - - - +
55A TYR* 3.8 24.9 - - - -
82A LEU* 2.8 25.2 + - - +
85A TYR* 1.3 77.6 - - - +
87A HIS* 1.3 61.2 + - - +
88A GLU* 3.8 2.3 + - - +
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Residues in contact with HIS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A TRP* 4.4 18.4 - + + -
48A THR* 4.1 4.9 - - - +
82A LEU 4.2 0.2 + - - -
83A CYS* 2.8 28.9 + - + +
84A LEU 4.7 1.6 - - - +
86A CYS* 1.3 79.3 - - - +
88A GLU* 1.3 69.0 + - + +
89A TYR* 3.1 35.4 + - + +
90A PHE* 3.1 16.0 + - + +
91A LYS 3.8 4.5 + - - -
10B ALA* 4.9 11.0 + - + +
13B VAL* 3.6 38.7 - - + +
14B CYS* 6.1 1.6 - - - -
17B GLN* 6.0 0.7 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il